From ef2a0171bc1e78d5c7221a1042c568f7cdfe149f Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 20 Oct 2025 17:16:33 +0200
Subject: [PATCH] Follow Python standard packaging guidelines

---
 .github/workflows/deploy.yml                           |  2 +-
 .github/workflows/pipeline.yml                         |  4 ++--
 pyproject.toml                                         | 10 +++++-----
 {pylammpsmpi => src/pylammpsmpi}/__init__.py           |  0
 {pylammpsmpi => src/pylammpsmpi}/_version.py           |  0
 {pylammpsmpi => src/pylammpsmpi}/mpi/__init__.py       |  0
 {pylammpsmpi => src/pylammpsmpi}/mpi/lmpmpi.py         |  0
 {pylammpsmpi => src/pylammpsmpi}/wrapper/__init__.py   |  0
 {pylammpsmpi => src/pylammpsmpi}/wrapper/ase.py        |  0
 {pylammpsmpi => src/pylammpsmpi}/wrapper/base.py       |  0
 {pylammpsmpi => src/pylammpsmpi}/wrapper/concurrent.py |  0
 {pylammpsmpi => src/pylammpsmpi}/wrapper/extended.py   |  0
 12 files changed, 8 insertions(+), 8 deletions(-)
 rename {pylammpsmpi => src/pylammpsmpi}/__init__.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/_version.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/mpi/__init__.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/mpi/lmpmpi.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/wrapper/__init__.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/wrapper/ase.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/wrapper/base.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/wrapper/concurrent.py (100%)
 rename {pylammpsmpi => src/pylammpsmpi}/wrapper/extended.py (100%)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 2a59bacd..17f937df 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -32,7 +32,7 @@ jobs:
       run: |
         cp .ci_support/environment-old.yml environment.yml
         python .ci_support/release.py; cat pyproject.toml
-        git update-index --assume-unchanged pyproject.toml pylammpsmpi/_version.py
+        git update-index --assume-unchanged pyproject.toml src/pylammpsmpi/_version.py
         hatchling build -t sdist -t wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
index b415ae68..4a990ee0 100644
--- a/.github/workflows/pipeline.yml
+++ b/.github/workflows/pipeline.yml
@@ -13,7 +13,7 @@ jobs:
     - uses: psf/black@stable
       with:
         options: "--check --diff"
-        src: ./${{ github.event.repository.name }}
+        src: ./src/${{ github.event.repository.name }}
 
   black_fix:  # in most cases pre-commit is faster
     needs: [black]
@@ -29,7 +29,7 @@ jobs:
       uses: psf/black@stable
       with:
         options: ""
-        src: "./${{ github.event.repository.name }}"
+        src: "./src/${{ github.event.repository.name }}"
     - name: commit
       run: |
         git config --local user.email "pyiron@mpie.de"
diff --git a/pyproject.toml b/pyproject.toml
index 66410112..a3e73e11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ include = [
 ]
 
 [tool.hatch.build.hooks.vcs]
-version-file = "pylammpsmpi/_version.py"
+version-file = "src/pylammpsmpi/_version.py"
 
 [tool.ruff]
 exclude = [".ci_support", "docs", "notebooks", "setup.py", "_version.py"]
@@ -90,18 +90,18 @@ ignore = [
 
 [tool.hatch.build.targets.sdist]
 include = [
-    "pylammpsmpi"
+    "src/pylammpsmpi"
 ]
 
 [tool.hatch.build.targets.wheel]
 packages = [
-    "pylammpsmpi"
+    "src/pylammpsmpi"
 ]
 
 [tool.hatch.version]
 source = "vcs"
-path = "pylammpsmpi/_version.py"
+path = "src/pylammpsmpi/_version.py"
 
 [tool.coverage.run]
-omit = ["pylammpsmpi/_version.py", "tests/*"]
+source = ["pylammpsmpi"]
 command_line = "-m unittest discover tests"
diff --git a/pylammpsmpi/__init__.py b/src/pylammpsmpi/__init__.py
similarity index 100%
rename from pylammpsmpi/__init__.py
rename to src/pylammpsmpi/__init__.py
diff --git a/pylammpsmpi/_version.py b/src/pylammpsmpi/_version.py
similarity index 100%
rename from pylammpsmpi/_version.py
rename to src/pylammpsmpi/_version.py
diff --git a/pylammpsmpi/mpi/__init__.py b/src/pylammpsmpi/mpi/__init__.py
similarity index 100%
rename from pylammpsmpi/mpi/__init__.py
rename to src/pylammpsmpi/mpi/__init__.py
diff --git a/pylammpsmpi/mpi/lmpmpi.py b/src/pylammpsmpi/mpi/lmpmpi.py
similarity index 100%
rename from pylammpsmpi/mpi/lmpmpi.py
rename to src/pylammpsmpi/mpi/lmpmpi.py
diff --git a/pylammpsmpi/wrapper/__init__.py b/src/pylammpsmpi/wrapper/__init__.py
similarity index 100%
rename from pylammpsmpi/wrapper/__init__.py
rename to src/pylammpsmpi/wrapper/__init__.py
diff --git a/pylammpsmpi/wrapper/ase.py b/src/pylammpsmpi/wrapper/ase.py
similarity index 100%
rename from pylammpsmpi/wrapper/ase.py
rename to src/pylammpsmpi/wrapper/ase.py
diff --git a/pylammpsmpi/wrapper/base.py b/src/pylammpsmpi/wrapper/base.py
similarity index 100%
rename from pylammpsmpi/wrapper/base.py
rename to src/pylammpsmpi/wrapper/base.py
diff --git a/pylammpsmpi/wrapper/concurrent.py b/src/pylammpsmpi/wrapper/concurrent.py
similarity index 100%
rename from pylammpsmpi/wrapper/concurrent.py
rename to src/pylammpsmpi/wrapper/concurrent.py
diff --git a/pylammpsmpi/wrapper/extended.py b/src/pylammpsmpi/wrapper/extended.py
similarity index 100%
rename from pylammpsmpi/wrapper/extended.py
rename to src/pylammpsmpi/wrapper/extended.py